TaLBD1, a LOB Transcription Factor Gene In T. Aestivum, Improves Plant N Starvation Adaptation Via Modulating N Acquisition-Associated Processes

Members of transcription factor (TF) families contribute largely to plant N starvation tolerance by regulating downstream stress defensive genes. In this study, we characterized TaLBD1, a Lateral Organ Boundary (LOB) TF gene in T. aestivum, in regulating plant low-N stress adaptation. TaLBD1 harbors the conserved domains specified by plant LOB proteins, targeting onto nucleus after endoplasmic reticulum (ER) assortment. The TaLBD1 transcripts were response sensitively to N starvation (NS) signaling, showing to be gradually upregulated in aerial and root tissues over a 27-h NS condition. The N. tabacum lines overexpressing TaLBD1 improved phenotype, root system architecture (RSA) establishment, biomass, and N contents of plants under NS treatment. The nitrate transporter gene NtNRT2.4 and PIN-FORMED gene NtPIN6 significantly upregulated in expression in NS-challenged lines; knockdown expression of NtNRT2.4 decreased N uptake and that of NtPIN6 alleviated RSA establishment relative to WT. These results validate the function of NRT and PIN genes in regulating plant N uptake and RSA behavior. RNA-seq analyses revealed that a quantity of genes modify expression in N-deprived lines overexpressing TaLBD1, which enriched into functional groups of signal transduction, transcription, protein biosynthesis, primary or secondary metabolism, and stress defensiveness. These findings suggested that the TaLBD1-improved NS adaptation attributes largely to its role in transcriptionally regulating NRT and PIN genes as well as in modulating those functional in various biological processes. TaLBD1 is a crucial regulator in plant N starvation tolerance and valuable target for molecular breeding high N use efficiency (NUE) crop cultivars.

The Novel Cucurbitaceae miRNA ClmiR86 Is Involved in Grafting-Enhanced Phosphate Utilization and Phosphate Starvation Tolerance in Watermelon

Watermelon (Citrullus lanatus) is a globally important Cucurbitaceae crop in which grafting is commonly used to improve stress tolerance and enhance nutrient utilization. However, the mechanism underlying grafting-enhanced nutrient assimilation remains unclear. Here, we demonstrate the possible involvement of a novel Cucurbitaceae miRNA, ClmiR86, in grafting-enhanced phosphate-starvation tolerance via CALCINEURIN B-LIKE INTERACTING PROTEIN KINASE 5 (ClCIPK5) suppression in watermelon. Transcript analyses revealed that the induction of ClmiR86 expression was correlated with the downregulation of ClCIPK5 in squash-grafted watermelon under phosphate starvation. In addition, the differential expression of ClmiR86 in various watermelon genotypes was consistent with their phosphate utilization efficiency. Furthermore, ClmiR86 overexpression in Arabidopsis enhanced root growth and phosphate uptake under phosphate starvation and promoted inflorescence elongation under normal conditions. These results suggest that the ClmiR86–ClCIPK5 axis is involved in phosphate starvation response as well as grafting-enhanced growth vigor and phosphate assimilation. The present study provides valuable insights for investigating long-distance signaling and nutrient utilization in plants.

Unique signals of clinal and seasonal allele frequency change at eQTLs in Drosophila melanogaster

Populations of short-lived organisms can respond to spatial and temporal environmental heterogeneity through local adaptation. Local adaptation can be reflected on both phenotypic and genetic levels, and it has been documented in many organisms. Although some complex fitness-related phenotypes have been shown to vary across latitudinal clines and seasons in similar ways in Drosophila melanogaster populations, we lack a general understanding of the genetic architecture of local adaptation across space and time. To address this problem, we examined patterns of allele frequency change across latitudinal clines and between seasons at previously reported expression quantitative trait loci (eQTLs). We divided eQTLs into groups by utilizing differential expression profiles of fly populations collected across a latitudinal cline or exposed to different environmental conditions. We also examined clinal and seasonal patterns of allele frequency change at eQTLs grouped by tissues. In general, we find that clinally varying polymorphisms are enriched for eQTLs, and that these eQTLs change in frequency in predictable ways across the cline and in response to starvation tolerance. The enrichment of eQTL among seasonally varying polymorphisms is more subtle, and the direction of allele frequency change at eQTL appears to be somewhat idiosyncratic. Taken together, we suggest that clinal adaptation at eQTLs is distinct than that of seasonal adaptation.

Neofunctionalization of a second insulin receptor gene in the wing-dimorphic planthopper, Nilaparvata lugens

A single insulin receptor (InR) gene has been identified and extensively studied in model species ranging from nematodes to mice. However, most insects possess additional copies of InR, yet the functional significance, if any, of alternate InRs is unknown. Here, we used the wing-dimorphic brown planthopper (BPH) as a model system to query the role of a second InR copy in insects. NlInR2 resembled the BPH InR homologue (NlInR1) in terms of nymph development and reproduction, but revealed distinct regulatory roles in fuel metabolism, lifespan, and starvation tolerance. Unlike a lethal phenotype derived from NlInR1 null, homozygous NlInR2 null mutants were viable and accelerated DNA replication and cell proliferation in wing cells, thus redirecting short-winged–destined BPHs to develop into long-winged morphs. Additionally, the proper expression of NlInR2 was needed to maintain symmetric vein patterning in wings. Our findings provide the first direct evidence for the regulatory complexity of the two InR paralogues in insects, implying the functionally independent evolution of multiple InRs in invertebrates.

Characterization of contrasting rice (Oryza sativa L.) genotypes reveals the Pi-efficient schema for phosphate starvation tolerance

Background Phosphorus (P), being one of the essential components of nucleic acids, cell membranes and enzymes, indispensable for diverse cellular processes like photosynthesis/carbohydrate metabolism, energy production, redox homeostasis and signaling. Crop yield is severely affected due to Phosphate (Pi) deficiency; and to cope with Pi-deficiency, plants have evolved several strategies. Some rice genotypes are compatible with low Pi availability, whereas others are sensitive to Pi deficiency. However, the underlying molecular mechanism for low Pi tolerance remains largely unexplored. Result Several studies were carried out to understand Pi-deficiency responses in rice at seedling stage, but few of them targeted molecular aspects/responses of Pi-starvation at the advanced stage of growth. To delineate the molecular mechanisms for low Pi tolerance, a pair of contrasting rice (Oryza sativa L.) genotypes [viz. Pusa-44 (Pi-deficiency sensitive) and its near isogenic line (NIL-23, Pi-deficiency tolerant) harboring Phosphorus uptake 1 (Pup1) QTL from an aus landrace Kasalath] were used. Comparative morphological, physiological, and biochemical analyses confirmed some of the well-known findings. Transcriptome analysis of shoot and root tissues from 45-day-old rice plants grown hydroponically under P-sufficient (16 ppm Pi) or P-starved (0 ppm Pi) medium revealed that Pi-starvation stress causes global transcriptional reprogramming affecting several transcription factors, signaling pathways and other regulatory genes. We could identify several significantly up-regulated genes in roots of NIL-23 under Pi-starvation which might be responsible for the Pi starvation tolerance. Pathway enrichment analysis indicated significant role of certain phosphatases, transporters, transcription factors, carbohydrate metabolism, hormone-signaling, and epigenetic processes in improving P-starvation stress tolerance in NIL-23. Conclusion We report the important candidate mechanisms for Pi acquisition/solubilization, recycling, remobilization/transport, sensing/signalling, genetic/epigenetic regulation, and cell wall structural changes to be responsible for P-starvation tolerance in NIL-23. The study provides some of the novel information useful for improving phosphorus-use efficiency in rice cultivars.

Genome-wide identification and expression analysis of autophagy genes in cucumber

Background Autophagy is an evolutionarily conserved physiological and developmental process in eukaryotes. In this process, damaged proteins in cells are degraded and cytoplasmic materials recycled. When plants are exposure to stress conditions or their growth and development are blocked, autophagy is induced to maintain the cell homeostasis by degrading long-lived proteins in the cells and organelles that function abnormally due to aging or damage. Cell autophagy has multiple functions in plants, it involved in growth and development, senescence, and responses to biotic and abiotic stress. So far, thirty three autophagy genes (ATG) have been found in rice, and more than 30 autophagy-related genes have been found in Arabidopsis, tobacco and corn, respectively. Four autophagy genes induced by salicylic acid were found in cucumber, but a little still unknown about all of autophagy genes in cucumber genome. Our experiment fully explored the ATG gene family of cucumber genome based on bioinformatics methods and identified 20 CsATG genes. We systematically analyzed the structure, conserved motifs, expression and phylogeny relationship of these ATG genes, which lays the foundation for exploring the function of the genes. Results A total of 20 putative ATG genes were identified in the cucumber genome. Gene duplication analysis showed that both fragmented and tandem duplication played vital roles in the amplification of cucumber ATG gene family. Gene expression analysis showed that 16 CsATG genes were induced by the salicylic acid (SA) treatment, and 16 CsATG genes were down-regulated by Methyl jasmonate (MeJA) treatment. Under high salinity stress, 10 CsATG genes were induced in roots. Under drought stress, 16 CsATG genes were induced in roots. Under carbon starvation stress, all of 20 CsATG genes were induced to express in leaves, suggesting that cell autophagy has a potential role in nutritional starvation tolerance. Conclusion Our results clearly have deepened our understanding of the characteristics and functions of cucumber ATG gene, and also found some new gene resources that can be used for the future development of cucumber and other crop varieties, which can resist stress.

Validating the automation of different measures of high temperature tolerance of small terrestrial insects

Accurately phenotyping numerous test subjects is essential for most experimental research. Collecting such data can be tedious or time-consuming, and can be biased or limited by manual observations. The thermal tolerance of small ectotherms is a good example of this type of phenotypic data, and it is widely used to investigate thermal adaptation, acclimation capacity and climate change resilience of small ectotherms. Here, we present the results of automatically generated thermal tolerance data using motion tracking on video recordings using two Drosophila species and temperature acclimation to create variation in thermal tolerances and two different heat tolerance assays. We find similar effect sizes of acclimation and hardening responses between manual and automated approaches, but different absolute tolerance estimates. This discrepancy likely reflects both technical differences and the behavioral cessation of movement rather than physiological failure measured in other assays. We conclude that both methods generate biological meaningful results, which reflect different aspects of the thermal biology, find no evidence of inflated variance in the manually scored assays, but find that automation can increase throughput without compromising quality. Further we show that the method can be applied to a wide range of arthropod taxa. We suggest that our automated method is a useful example of through-put phenotyping, and suggest this approach might be applied to other tedious laboratory traits, such as desiccation or starvation tolerance, with similar benefits to through-put. However, the interpretation and potential comparison to results using different methodology rely on thorough validation of the assay and the involved biological mechanism.

PPi plays a role in sugar starvation tolerance

H+-PPase acidifies the endo-membrane compartments utilizing the energy of PPi hydrolysis. This acidification creates an electrochemical proton gradient that powers the secondary active transport and allows for vacuolar accumulation of several materials against their concentration gradients. The hydrolysis of the cytosolic PPi is necessary for the forwardness of the PPi-generating reactions. However, information is lacking on the role of PPi in adaptation to sugar starvation and low energy status in plants. Here, several mutants lacking the functional H+-PPases were used to illuminate this role. Three alleles of fugu5 mutants defective in type I H+-PPase exhibited better tolerance to sugar starvation than wild-type plants, when grown on ½ and full-strength MS media under photosynthesis-constraining low light intensity. The PPi level in fugu5 mutants was significantly higher than its level in wild type and type II H+-PPase-defective mutants. SnRK1 (Sucrose-non-fermenting1-Related kinase-1) plays a central role in the coordination of the plant transcriptome to the energy signals. SnRK1 senses the energy depletion in plant cells, and controls the expression of genes and phosphorylation of proteins in a way that promotes catabolism, and inhibits anabolism. Sugar starvation significantly induced the SnRK1 phosphorylation activity in wild type and type II H+-PPase lacking mutants. Whereas the activity remained unchanged in sugar-starved fugu5 mutants. This is possibly achieved through activation of PPi-dependent enzymes. Results suggest that the high PPi level in fugu5 mutants might contribute to more efficiently use of low level of ATP under sugar starvation and low light conditions.